X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignFrameTest.java;h=454ff610f3c62db8c5c53f00a8fb92d23cae0466;hb=refs%2Fheads%2Ffeature%2FJAL-3251biotypedMappings;hp=dd1a4dedc667f59b426e47804f4dbf7004655f86;hpb=ad09c54f294b945fd4d037a93f5fa8eced6c1797;p=jalview.git

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index dd1a4de..454ff61 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -20,25 +20,29 @@
  */
 package jalview.gui;
 
+import static org.junit.Assert.assertNotEquals;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.Jalview2xmlTests;
+import jalview.project.Jalview2xmlTests;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.FeatureColour;
 import jalview.schemes.HelixColourScheme;
 import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.StrandColourScheme;
@@ -69,26 +73,34 @@ public class AlignFrameTest
   {
     SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
     SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
-    seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5,
-            Float.NaN, null));
-    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10,
-            Float.NaN, null));
+    seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
+    seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
+            null));
     seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
             Float.NaN, null));
     seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
             Float.NaN, null));
     AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
-    AlignFrame alignFrame = new AlignFrame(al, al.getWidth(), al.getHeight());
+    AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
+            al.getHeight());
+
+    /*
+     * make all features visible (select feature columns checks visibility)
+     */
+    alignFrame.getFeatureRenderer().findAllFeatures(true);
 
     /*
      * hiding a feature not present does nothing
      */
     assertFalse(alignFrame.hideFeatureColumns("exon", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+
     assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
             .getNumberOfRegions(), 0);
+
     assertFalse(alignFrame.hideFeatureColumns("exon", false));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+
     assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
             .getNumberOfRegions(), 0);
 
@@ -97,20 +109,41 @@ public class AlignFrameTest
      */
     assertFalse(alignFrame.hideFeatureColumns("Metal", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
+
     assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
             .getNumberOfRegions(), 0);
 
+
+    /*
+     * threshold Metal to hide features where score < 5
+     * seq1 feature in columns 1-5 is hidden
+     * seq2 feature in columns 6-10 is shown
+     */
+    FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+            0f, 10f);
+    fc.setAboveThreshold(true);
+    fc.setThreshold(5f);
+    alignFrame.getFeatureRenderer().setColour("Metal", fc);
+    assertTrue(alignFrame.hideFeatureColumns("Metal", true));
+    HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
+    assertEquals(hidden.getNumberOfRegions(), 1);
+    Iterator<int[]> regions = hidden.iterator();
+    int[] next = regions.next();
+    assertEquals(next[0], 5);
+    assertEquals(next[1], 9);
+
     /*
      * hide a feature present in some columns
      * sequence positions [2-4], [7-9] are column positions
      * [1-3], [6-8] base zero
      */
+    alignFrame.getViewport().showAllHiddenColumns();
     assertTrue(alignFrame.hideFeatureColumns("Turn", true));
-    Iterator<int[]> regions = alignFrame.getViewport().getAlignment()
+    regions = alignFrame.getViewport().getAlignment()
             .getHiddenColumns().iterator();
     assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
             .getNumberOfRegions(), 2);
-    int[] next = regions.next();
+    next = regions.next();
     assertEquals(next[0], 1);
     assertEquals(next[1], 3);
     next = regions.next();
@@ -568,4 +601,26 @@ public class AlignFrameTest
     sp.valueChanged(22);
     assertEquals(av2.getResidueShading().getConservationInc(), 22);
   }
+
+  /**
+   * Verify that making a New View preserves the dataset reference for the
+   * alignment. Otherwise, see a 'duplicate jar entry' reference when trying to
+   * save alignments with multiple views, and codon mappings will not be shared
+   * across all panels in a split frame.
+   * 
+   * @see Jalview2xmlTests#testStoreAndRecoverColourThresholds()
+   */
+  @Test(groups = "Functional")
+  public void testNewView_dsRefPreserved()
+  {
+    AlignViewport av = af.getViewport();
+    AlignmentI al = av.getAlignment();
+    AlignmentI original_ds = al.getDataset();
+    af.newView_actionPerformed(null);
+    assertNotEquals("New view didn't select the a new panel", av,
+            af.getViewport());
+    org.testng.Assert.assertEquals(original_ds,
+            af.getViewport().getAlignment().getDataset(),
+            "Dataset was not preserved in new view");
+  }
 }